\section{Figure Instructions} \label{appendix:figureinstructions}

To make the figures in this thesis, one needs to checkout our nucnet-projects
code and install certain libraries to compile our code. The instructions of
installing these libraries can be found at Dr. Meyer's tutorial:
\url{http://sourceforge.net/u/mbradle/wiki}

After install the necessary libraries, just create a projects directory:
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\texttt{mkdir projects}
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Change into the projects directory:
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\texttt{cd projects}
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Now checkout the project:
\footnote{The code sits on assembla.com temporarily and will be moved to 
sourceforge.net eventually.}
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\texttt{svn checkout https://subversion.assembla.com/svn/simple-Ia/trunk simple-Ia}
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Now change into the project directory and compile the code:
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\texttt{cd simple-Ia}
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\texttt{make all\_Ia}
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Upon successful compilation, there will be executables like {\tt run\_entropy}.
Then download the data files:
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\texttt{make data}
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Then one can run the simple Ia calculation. For example to run a calculation
with initial density of $9\times 10^9 g/cm^3$, initial temperature of
$1.5\times 10^9K$, star mass of 1.5 solar mass and only consider nuclei with
proton number equal or smaller than 50: 
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\texttt{./run\_entropy ../nucnet-tools/data\_pub/my\_net.xml zone.xml 
  out\_9.0e9.xml 9.e9 "[z <= 50]"}
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The initial temperature and star mass are set in \texttt{zone.xml}. Also
there are several other parameters that can be set in the xml file, like
end time, initial time step, neutrino chemical potential, whether to use
approximate weak rates, whether to include neutrino/photon entropy loss, 
whether to use screening, whether to use detailed weak rates, etc.
After got an output xml file (\texttt{out\_9.0e9.xml} in the example 
above), one can use the nucnet-tools examples to analyze it. To do this,
the analysis examples need to be compiled:
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\texttt{cd ../nucnet-tools/examples/analysis}
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\texttt{make all\_analysis}
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\texttt{cd -}

Now let's look at the instructions for making each figure.

%===============================================================================
% Start figure instructions.
%===============================================================================

\newcommand{\thisFigure}{null}
\newcommand{\outFile}{null}
\newcommand{\thisRun}{out\_9.0e9.xml}

\input{appendix/x_fig}
\input{appendix/v_fig}
\input{appendix/T_fig}

